This notebook will begin looking at clustering methods on the expression of the genes in a single sample of the dataset of interest, from an unbiased approach.
# Load libraries
library(magrittr)
library(scater)
library(readr)
library(bluster)
library(ggpubr)
library(pheatmap)
# Set file paths
data_dir <- file.path("results", "Gawad_processed_data")
# Source custom functions script
source(file.path("utils", "clustering-functions.R"))
sample_290_normalized <- read_rds(
file.path(data_dir, "SCPCS000216", "SCPCL000290_miQC_downstream_processed_normalized_reduced_sce.rds"))
# Perform k-means clustering
kmeans_cluster_names <- paste("kmeans", c(4:10), sep = "_")
sample_290_normalized <- kmeans_clustering(
sample_290_normalized,
k_range = c(4:10),
check_stability = TRUE
)
# Plot k-means
kmeans_plot_list <- kmeans_cluster_names %>%
purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + theme_bw())
cowplot::plot_grid(plotlist = kmeans_plot_list, ncol = 4)
# Perform graph-based walktrap clustering
walktrap_cluster_names <- paste("walktrap", c(5, 10, 15, 20, 25), sep = "_")
sample_290_normalized <- graph_clustering(
sample_290_normalized,
nn_range = c(5, 10, 15, 20, 25),
weighting_type = "rank",
cluster_function = "walktrap",
check_stability = TRUE
)
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
# Plot
walktrap_plot_list <- walktrap_cluster_names %>%
purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + theme_bw())
cowplot::plot_grid(plotlist = walktrap_plot_list, ncol = 3)
# Perform graph-based louvain clustering
louvain_cluster_names <- paste("louvain", c(5, 10, 15, 20, 25), sep = "_")
sample_290_normalized <- graph_clustering(
sample_290_normalized,
nn_range = c(5, 10, 15, 20, 25),
weighting_type = "jaccard",
cluster_function = "louvain",
check_stability = TRUE
)
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn, :
detected tied distances to neighbors, see ?'BiocNeighbors-ties'
# Plot
louvain_plot_list <- louvain_cluster_names %>%
purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + theme_bw())
cowplot::plot_grid(plotlist = louvain_plot_list, ncol = 3)
# Check the k-means cluster validity stats for each of the clusters and return
# stats in a data frame
kmeans_stats_df <- create_metadata_stats_df(sample_290_normalized, c(4:10), 1, "kmeans")
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
# Preview the results
head(kmeans_stats_df)
# Summarize the stats and return in a data frame
kmeans_summary_stats_df <- summarize_clustering_stats(kmeans_stats_df)
# Preview the summary results
head(kmeans_summary_stats_df)
# Plot individual cluster purity stats
kmeans_purity_plots <- plot_cluster_purity(kmeans_stats_df)
kmeans_purity_plots
# Plot individual cluster silhouette width stats
kmeans_silhouette_plots <- plot_cluster_silhouette_width(kmeans_stats_df)
kmeans_silhouette_plots
# Check the walktrap cluster validity stats for each of the clusters and return
# stats in a data frame
walktrap_stats_df <- create_metadata_stats_df(sample_290_normalized, c(5:25), 5, "walktrap")
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
# Preview the all stats results
head(walktrap_stats_df)
# Summarize the stats and return in a data frame
walktrap_summary_stats_df <- summarize_clustering_stats(walktrap_stats_df)
# Preview the summary results
head(walktrap_summary_stats_df)
# Plot individual cluster purity stats
walktrap_purity_plots <- plot_cluster_purity(walktrap_stats_df)
walktrap_purity_plots
# Plot individual cluster silhouette width stats
walktrap_silhouette_plots <- plot_cluster_silhouette_width(walktrap_stats_df)
walktrap_silhouette_plots
# Check the louvain cluster validity stats for each of the clusters and return
# stats in a data frame
louvain_stats_df <- create_metadata_stats_df(sample_290_normalized, c(5:25), 5, "louvain")
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
# Preview the results
head(louvain_stats_df)
# Summarize the stats and return in a data frame
louvain_summary_stats_df <- summarize_clustering_stats(louvain_stats_df)
# Preview the summary results
head(louvain_summary_stats_df)
# Plot individual cluster purity stats
louvain_purity_plots <- plot_cluster_purity(louvain_stats_df)
louvain_purity_plots
# Plot individual cluster silhouette width stats
louvain_silhouette_plots <- plot_cluster_silhouette_width(louvain_stats_df)
louvain_silhouette_plots
# Check and plot cluster stability
kmeans_cluster_names %>%
purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))
walktrap_cluster_names %>%
purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))
louvain_cluster_names %>%
purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8
[6] LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] pheatmap_1.0.12 ggpubr_0.4.0 bluster_1.4.0 readr_2.1.1
[5] scater_1.22.0 ggplot2_3.3.5 scuttle_1.4.0 SingleCellExperiment_1.16.0
[9] SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.0
[13] IRanges_2.28.0 S4Vectors_0.32.3 BiocGenerics_0.40.0 MatrixGenerics_1.6.0
[17] matrixStats_0.61.0 magrittr_2.0.1
loaded via a namespace (and not attached):
[1] bitops_1.0-7 RColorBrewer_1.1-2 bslib_0.3.1 tools_4.1.2
[5] backports_1.4.0 utf8_1.2.2 R6_2.5.1 irlba_2.3.3
[9] vipor_0.4.5 DBI_1.1.1 colorspace_2.0-2 nnet_7.3-16
[13] withr_2.4.3 tidyselect_1.1.1 gridExtra_2.3 compiler_4.1.2
[17] cli_3.1.0 BiocNeighbors_1.12.0 DelayedArray_0.20.0 sass_0.4.0
[21] labeling_0.4.2 scales_1.1.1 stringr_1.4.0 digest_0.6.29
[25] rmarkdown_2.11 XVector_0.34.0 pkgconfig_2.0.3 htmltools_0.5.2
[29] sparseMatrixStats_1.6.0 fastmap_1.1.0 rlang_0.4.12 rstudioapi_0.13
[33] DelayedMatrixStats_1.16.0 jquerylib_0.1.4 farver_2.1.0 generics_0.1.1
[37] jsonlite_1.7.2 BiocParallel_1.28.2 dplyr_1.0.7 car_3.0-12
[41] RCurl_1.98-1.5 BiocSingular_1.10.0 modeltools_0.2-23 GenomeInfoDbData_1.2.7
[45] Matrix_1.3-4 Rcpp_1.0.7 ggbeeswarm_0.6.0 munsell_0.5.0
[49] fansi_0.5.0 abind_1.4-5 viridis_0.6.2 lifecycle_1.0.1
[53] stringi_1.7.6 yaml_2.2.1 carData_3.0-4 zlibbioc_1.40.0
[57] flexmix_2.3-17 grid_4.1.2 parallel_4.1.2 ggrepel_0.9.1
[61] crayon_1.4.2 lattice_0.20-45 cowplot_1.1.1 beachmat_2.10.0
[65] splines_4.1.2 hms_1.1.1 knitr_1.36 pillar_1.6.4
[69] igraph_1.2.9 ggsignif_0.6.3 ScaledMatrix_1.2.0 glue_1.5.1
[73] evaluate_0.14 renv_0.14.0 vctrs_0.3.8 tzdb_0.2.0
[77] gtable_0.3.0 purrr_0.3.4 tidyr_1.1.4 assertthat_0.2.1
[81] xfun_0.28 rsvd_1.0.5 broom_0.7.10 miQC_1.2.0
[85] rstatix_0.7.0 viridisLite_0.4.0 tibble_3.1.6 beeswarm_0.4.0
[89] cluster_2.1.2 ellipsis_0.3.2